Variant report

Variant	rs13004057
Chromosome Location	chr2:133887421-133887422
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10803536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10928441	0.93[ASN][1000 genomes]
rs10928442	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12052593	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12053035	0.96[ASN][1000 genomes]
rs12611686	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613747	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12621765	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12622633	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624035	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12991216	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12996075	0.96[ASN][1000 genomes]
rs13001406	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13021439	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13031924	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1434225	0.95[ASN][1000 genomes]
rs1434228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16857026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16857027	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16857341	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs16857667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16857684	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16857813	0.95[ASN][1000 genomes]
rs16857829	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16857909	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16857911	0.95[ASN][1000 genomes]
rs1975218	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1975219	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975220	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975221	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2117307	0.92[ASN][1000 genomes]
rs2117308	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2217748	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278454	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278455	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278456	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34497516	0.91[ASN][1000 genomes]
rs34962273	0.86[ASN][1000 genomes]
rs35101763	0.91[ASN][1000 genomes]
rs35385294	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35559119	0.90[ASN][1000 genomes]
rs35635401	0.97[ASN][1000 genomes]
rs35976316	0.96[ASN][1000 genomes]
rs35986779	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283469	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4953871	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953874	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4954027	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4954028	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4954030	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs4954033	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6430394	0.96[ASN][1000 genomes]
rs6430397	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs6430398	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6715483	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722768	0.87[YRI][hapmap]
rs6733792	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735052	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735119	0.89[YRI][hapmap]
rs6744186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6744536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6749758	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6753721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs71413533	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71413534	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71413537	0.86[ASN][1000 genomes]
rs71413541	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71413543	0.95[ASN][1000 genomes]
rs71413544	0.96[ASN][1000 genomes]
rs7568295	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7585526	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7588673	0.80[AFR][1000 genomes]
rs7592507	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597720	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834382	chr2:133728399-133891418	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875139	chr2:133777866-133929225	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv949546	chr2:133798832-133933491	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv875140	chr2:133816484-133904829	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1008004	chr2:133827250-133954810	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv949629	chr2:133830379-134014961	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1001601	chr2:133838626-134005959	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv948851	chr2:133864452-133955999	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv583167	chr2:133864452-133957689	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv834383	chr2:133874257-133906766	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133854800-133892000	Weak transcription	Left Ventricle	heart
2	chr2:133868000-133888200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:133880000-133889200	Weak transcription	Liver	Liver
4	chr2:133880400-133888800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:133880400-133889000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:133880600-133896200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:133881800-133889200	Weak transcription	Ovary	ovary
8	chr2:133882000-133888600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:133882400-133889000	Weak transcription	Fetal Stomach	stomach
10	chr2:133883800-133887800	Weak transcription	Hela-S3	cervix
11	chr2:133884400-133896600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:133884800-133887800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:133885400-133888600	Weak transcription	NH-A	brain
14	chr2:133885800-133888600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:133885800-133897800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:133886400-133888200	Weak transcription	Osteobl	bone
17	chr2:133886400-133888400	Weak transcription	NHLF	lung
18	chr2:133887200-133887800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:133887200-133887800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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